You still need to have all of the bashed mods active. The bashed patch doesn't replicate what's in the individual mods, but rather it creates a set of overrides and such that will help to resolve a lot of conflicts between mods. Make sure you also update your masters with the bashed patch activated.

Nope, it will pop up with a prompt when you make your patch and it will tell which mods can be merged into the patch. If you allow it to do so, you can safely disable those mods if bash doesn't do it for you automatically. If the patch has any dependencies then no, you cannot disable those mods.